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The club was founded in 1960 under name Bukhoro. In 1989 club was renamed to Nurafshon. During the 1990 season the club played in the Soviet Second League, zone "East", finishing in 4th position. Buxoro played its first Oliy League season in 1992. The best club performance in Oliy League is runners-up of 1994 season after Neftchi Farg'ona.
FK Bukhoro played three times in semi-final of Uzbek Cup. In 2005 Cup semi-final club lost to Neftchi Farg'ona in two legs by 1–3 and in 2012 lost to Nasaf with a 3–5 score. After the 2013 season had finished, on 10 November 2013 Edgar Gess became new head coach of Bukhoro, replacing Tachmurad Agamuradov in this position.